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This page was generated on 2021-09-24 15:06:04 -0400 (Fri, 24 Sep 2021).

CHECK results for CAGEr on tokay2

To the developers/maintainers of the CAGEr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.git to
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raw results

Package 231/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.34.0  (landing page)
Charles Plessy
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_13
git_last_commit: 8e7ccda
git_last_commit_date: 2021-05-19 11:57:42 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CAGEr_1.34.0.tar.gz
StartedAt: 2021-09-23 19:54:57 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 20:07:12 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 735.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CAGEr.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CAGEr_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '1.34.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CAGEr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpcP5n8D/R.INSTALL1d8c7a847bef/CAGEr/man/CustomConsensusClusters.Rd:42: missing link '.ConsensusClusters'
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpcP5n8D/R.INSTALL1d8c7a847bef/CAGEr/man/clusterCTSS.Rd:89: missing link 'TagClusters'
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpcP5n8D/R.INSTALL1d8c7a847bef/CAGEr/man/consensusClusters.Rd:52: missing link 'ConsensusClusters'
  Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpcP5n8D/R.INSTALL1d8c7a847bef/CAGEr/man/tagClusters.Rd:58: missing link 'TagClusters'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'CustomConsensusClusters.Rd':
  '.ConsensusClusters'

Missing link or links in documentation object 'clusterCTSS.Rd':
  'TagClusters'

Missing link or links in documentation object 'consensusClusters.Rd':
  'ConsensusClusters'

Missing link or links in documentation object 'tagClusters.Rd':
  'TagClusters'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'show' and siglist 'CTSS'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'CTSS-class'
  '.Object' '...' 'bsgenomeName' 'seqnames' 'pos' 'strand' 'seqinfo'
  'seqlengths' 'from' 'to' 'strict'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
importPublicData           37.18   1.54   48.34
scoreShift                 27.19   0.06   27.27
cumulativeCTSSdistribution 21.80   4.80   26.59
quantilePositions          21.32   0.49   21.80
aggregateTagClusters       11.13   0.00   11.12
CAGEexp-class               6.05   1.25    7.56
distclu-functions           5.89   0.54    6.44
clusterCTSS                 5.40   0.25    5.66
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
scoreShift                 33.06   0.07   33.12
importPublicData           26.24   1.45   32.86
cumulativeCTSSdistribution 21.53   5.94   27.47
quantilePositions          22.68   0.58   23.27
aggregateTagClusters       17.30   0.01   17.32
distclu-functions           5.59   0.80    6.41
CAGEexp-class               5.03   0.97    6.00
clusterCTSS                 5.66   0.28    5.94
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck/00check.log'
for details.



Installation output

CAGEr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CAGEr_1.34.0.tar.gz && rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAGEr.buildbin-libdir CAGEr_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CAGEr_1.34.0.zip && rm CAGEr_1.34.0.tar.gz CAGEr_1.34.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  773k  100  773k    0     0  1589k      0 --:--:-- --:--:-- --:--:-- 1594k

install for i386

* installing *source* package 'CAGEr' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CAGEr'
    finding HTML links ... done
    CAGEexp-class                           html  
    finding level-2 HTML links ... done

    CAGEr-class                             html  
    CAGEr-package                           html  
    CAGEr_Multicore                         html  
    CAGEset-class                           html  
    CTSS-class                              html  
    CTSSclusteringMethod                    html  
    CTSScoordinates                         html  
    CTSScumulativesTagClusters              html  
    CTSSnormalizedTpm                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.buildbin-libdir/00LOCK-CAGEr/00new/CAGEr/help/CTSSnormalizedTpmDF.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.buildbin-libdir/00LOCK-CAGEr/00new/CAGEr/help/CTSSnormalizedTpmDF+2CCAGEset-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.buildbin-libdir/00LOCK-CAGEr/00new/CAGEr/help/CTSSnormalizedTpmDF+2CCAGEexp-method.html
    CTSStagCount                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.buildbin-libdir/00LOCK-CAGEr/00new/CAGEr/help/CTSStagCountDF.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.buildbin-libdir/00LOCK-CAGEr/00new/CAGEr/help/CTSStagCountDF+2CCAGEset-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.buildbin-libdir/00LOCK-CAGEr/00new/CAGEr/help/CTSStagCountDF+2CCAGEexp-method.html
    CTSStagCountTable                       html  
    CTSStoGenes                             html  
    CustomConsensusClusters                 html  
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpcP5n8D/R.INSTALL1d8c7a847bef/CAGEr/man/CustomConsensusClusters.Rd:42: missing link '.ConsensusClusters'
    FANTOM5humanSamples                     html  
    FANTOM5mouseSamples                     html  
    GeneExpDESeq2                           html  
    GeneExpSE                               html  
    QuantileWidthFunctions                  html  
    aggregateTagClusters                    html  
    annotateCTSS                            html  
    bam2CTSS                                html  
    byCtss                                  html  
    clusterAggregateAndSum                  html  
    clusterCTSS                             html  
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpcP5n8D/R.INSTALL1d8c7a847bef/CAGEr/man/clusterCTSS.Rd:89: missing link 'TagClusters'
    coerceInBSgenome                        html  
    consensusClusterConvertors              html  
    consensusClusters-set                   html  
    consensusClusters                       html  
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpcP5n8D/R.INSTALL1d8c7a847bef/CAGEr/man/consensusClusters.Rd:52: missing link 'ConsensusClusters'
    consensusClustersDESeq2                 html  
    consensusClustersQuantile               html  
    consensusClustersTpm                    html  
    coverage-functions                      html  
    cumulativeCTSSdistribution              html  
    distclu-functions                       html  
    exampleCAGEexp                          html  
    exampleCAGEset                          html  
    exampleZv9_annot                        html  
    exportCTSStoBedGraph                    html  
    exportToBed                             html  
    expressionClasses                       html  
    extractExpressionClass                  html  
    genomeName                              html  
    getCTSS                                 html  
    getExpressionProfiles                   html  
    getShiftingPromoters                    html  
    hanabi-class                            html  
    hanabi                                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.buildbin-libdir/00LOCK-CAGEr/00new/CAGEr/help/hanabi+2Clist-method.html
    hanabiPlot                              html  
    import.CAGEscanMolecule                 html  
    import.CTSS                             html  
    import.bam                              html  
    import.bam.ctss                         html  
    import.bedCTSS                          html  
    import.bedScore                         html  
    import.bedmolecule                      html  
    importPublicData                        html  
    inputFiles                              html  
    inputFilesType                          html  
    librarySizes                            html  
    loadFileIntoGPos                        html  
    mapStats                                html  
    mapStatsScopes                          html  
    mergeCAGEsets                           html  
    mergeSamples                            html  
    moleculesGR2CTSS                        html  
    normalizeTagCount                       html  
    parseCAGEscanBlocksToGrangeTSS          html  
    plot.hanabi                             html  
    plotAnnot                               html  
    plotCorrelation                         html  
    plotExpressionProfiles                  html  
    plotInterquantileWidth                  html  
    plotReverseCumulatives                  html  
    powerLaw                                html  
    quantilePositions                       html  
    ranges2annot                            html  
    ranges2genes                            html  
    ranges2names                            html  
    sampleLabels                            html  
    scoreShift                              html  
    seqNameTotalsSE                         html  
    setColors                               html  
    show-methods                            html  
    strandInvaders                          html  
    summariseChrExpr                        html  
    tagClusterConvertors                    html  
    tagClusters                             html  
Rd warning: C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpcP5n8D/R.INSTALL1d8c7a847bef/CAGEr/man/tagClusters.Rd:58: missing link 'TagClusters'
    tagClustersQuantile                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CAGEr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.34.0.zip
* DONE (CAGEr)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CAGEr' successfully unpacked and MD5 sums checked

Tests output


Example timings

CAGEr.Rcheck/examples_i386/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class6.051.257.56
CAGEr_Multicore0.030.010.05
CAGEset-class000
CTSS-class0.260.030.30
CTSSclusteringMethod0.020.000.01
CTSScoordinates0.090.000.10
CTSSnormalizedTpm0.860.000.86
CTSStagCount0.240.000.23
CTSStagCountTable000
CTSStoGenes0.680.000.69
CustomConsensusClusters1.210.001.20
GeneExpDESeq21.180.051.24
GeneExpSE000
QuantileWidthFunctions000
aggregateTagClusters11.13 0.0011.12
annotateCTSS1.550.021.56
byCtss000
clusterCTSS5.400.255.66
consensusClusterConvertors0.030.000.03
consensusClusters2.580.402.99
consensusClustersDESeq20.280.000.28
consensusClustersTpm000
coverage-functions3.160.413.56
cumulativeCTSSdistribution21.80 4.8026.59
distclu-functions5.890.546.44
exampleCAGEexp000
exampleCAGEset000
exportCTSStoBedGraph2.780.002.78
exportToBed2.440.022.45
expressionClasses000
extractExpressionClass000
genomeName000
getCTSS0.140.010.18
getExpressionProfiles0.320.000.32
getShiftingPromoters000
hanabi0.460.040.49
hanabiPlot1.370.001.37
import.CAGEscanMolecule000
import.CTSS0.10.00.1
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData37.18 1.5448.34
inputFiles0.020.000.02
inputFilesType000
librarySizes000
mapStats0.050.000.04
mergeCAGEsets2.860.173.04
mergeSamples0.850.000.85
moleculesGR2CTSS0.150.000.15
normalizeTagCount0.760.000.76
parseCAGEscanBlocksToGrangeTSS0.030.000.03
plotAnnot2.350.022.36
plotCorrelation0.560.000.56
plotExpressionProfiles0.170.000.18
plotInterquantileWidth0.810.030.84
plotReverseCumulatives0.530.000.53
quantilePositions21.32 0.4921.80
ranges2annot0.370.000.37
ranges2genes0.050.000.05
ranges2names0.060.000.06
sampleLabels000
scoreShift27.19 0.0627.27
seqNameTotalsSE000
setColors1.30.21.5
strandInvaders1.980.192.39
summariseChrExpr0.690.000.69
tagClusterConvertors0.360.000.36
tagClusters0.060.000.06

CAGEr.Rcheck/examples_x64/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class5.030.976.00
CAGEr_Multicore0.070.000.06
CAGEset-class0.010.000.02
CTSS-class0.390.000.39
CTSSclusteringMethod0.020.000.02
CTSScoordinates0.190.000.18
CTSSnormalizedTpm1.260.001.27
CTSStagCount0.280.000.28
CTSStagCountTable0.020.000.02
CTSStoGenes0.720.000.71
CustomConsensusClusters1.900.001.91
GeneExpDESeq22.020.082.09
GeneExpSE000
QuantileWidthFunctions000
aggregateTagClusters17.30 0.0117.32
annotateCTSS2.030.002.03
byCtss0.010.000.01
clusterCTSS5.660.285.94
consensusClusterConvertors0.030.000.03
consensusClusters2.080.462.53
consensusClustersDESeq20.280.000.29
consensusClustersTpm000
coverage-functions3.470.433.90
cumulativeCTSSdistribution21.53 5.9427.47
distclu-functions5.590.806.41
exampleCAGEexp000
exampleCAGEset0.020.000.01
exportCTSStoBedGraph3.390.013.41
exportToBed3.080.003.08
expressionClasses000
extractExpressionClass0.010.000.01
genomeName000
getCTSS0.110.020.13
getExpressionProfiles0.260.000.27
getShiftingPromoters0.020.000.01
hanabi0.360.000.36
hanabiPlot0.530.000.53
import.CAGEscanMolecule000
import.CTSS0.090.000.10
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData26.24 1.4532.86
inputFiles000
inputFilesType000
librarySizes000
mapStats0.050.000.04
mergeCAGEsets3.210.053.27
mergeSamples0.940.000.94
moleculesGR2CTSS0.140.000.14
normalizeTagCount0.860.000.86
parseCAGEscanBlocksToGrangeTSS0.020.000.01
plotAnnot2.140.022.16
plotCorrelation0.610.000.60
plotExpressionProfiles0.160.000.16
plotInterquantileWidth0.940.000.94
plotReverseCumulatives0.890.000.89
quantilePositions22.68 0.5823.27
ranges2annot0.430.000.42
ranges2genes0.060.000.06
ranges2names0.050.000.05
sampleLabels000
scoreShift33.06 0.0733.12
seqNameTotalsSE000
setColors1.470.001.47
strandInvaders1.070.041.11
summariseChrExpr0.650.000.65
tagClusterConvertors0.360.000.36
tagClusters0.050.000.05